Bacterial carbon production is an important parameter in understanding the flows of carbon and energy in aquatic ecosystems, but has been difficult to measure. Present methods are based on measuring the rate of cell production, and thus require a knowledge of cellular carbon content of the growing bacteria to convert cell production into carbon production. We have examined the possibility that protein synthesis rate of pelagic bacteria might serve as the basis for directly estimating bacterial carbon production. We measured bacterial protein content and protein production of pelagic bacteria. Bacterial protein content was measured as amino acids by high performance liquid chromatography of cell hydrolysates of bacterial assemblages of mean diameters from 0.026 to 0.4 km. Cellular protein:volume (w/v) in the largest bacteria was 15.2 '10 (similar to cultured Escherichia coli] but increased with decreasing cell size to 46.5 % in 0.026 pm bacteria. Protein per bacterium was correlated with cell volume by the power function y = 8 8 .~2~' (r2 = 0.67; p C 0.01; n = 25). An inventory of major bacterial macromolecular pools revealed that cell protein:dry weight and cell protein:carbon were essentially constant (63 % and 54 %. respectively) for the entire cell size range although cell protein:volume increased with decreasing cell size. Thus, the smaller cells in the size range were rich in carbon and dry weight and poor in water compared with larger cells. We established the experimental conditions for estimating protein synthesis on the basis of 3H leucine incorporation by bacteria, and determined the necessary parameters (including the intracellular isotope dilution by HPLC) for converting 3~ leucine incorporation into protein synthesis rate. In samples from Scripps Institution of Oceanography pier the intracellular isotope dilution was only 2-fold. In a field study in Southern California Bight bacterial protein production and %I-thymidine incorporation methods yielded comparable rates of bacterial production. Bacterial protein production method was an order of magnitude more sensitive and yielded bacterial carbon production directly without the need to know the cell size of the part of the assemblage in growth state.

Macroscopic organic aggregates, which are > 500 µm and known as marine and lake snow, are important components in the turnover, decomposition and sinking flux of both organic and inorganic matter and elements in aquatic ecosystems. They are composed of various organic and inorganic materials depending largely on the given system and environmental conditions. The systems include the pelagic limnetic, the neritic and oceanic marine region, as well as shallow turbid environments, e.g. rivers, the littoral zone of lakes, estuaries and tidally affected coastal areas with intense turbulence and a high load of suspended matter. Aggregate abundance and size vary greatly among these systems. Macroaggregates are heavily colonized by bacteria and other heterotrophic microbes and greatly enriched in organic and inorganic nutrients as compared to the surrounding water. During the last 15 yr, many studies have been carried out to examine various aspects of the formation of aggregates, their microbial colonization and decomposition, nutrient recycling and their significance for the sinking flux. They have been identified as hot-spots of the microbial decomposition of organic matter. Further, microaggregates, which are < 5 to 500 µm in size and stained by different dyes, such as transparent exopolymer particles (TEP) and Coomassie blue-stained particles, have been discovered and shown also to be important in the formation and decomposition of macroaggregates. In this review we give an overview of the present state of the microbial ecology of macro-and microaggregates, including the mentioned points but highlighting in particular the recent findings on the bacterial colonization of aggregates using molecular tools, their microbial decomposition and mineralization, and the significance of protozoans and metazoans for the colonization and decomposition of macroaggregates. Today it is evident that not only the aggregates but also their surroundings are sites and hot-spots of microbial processes, with the plume of solutes leaking out of the aggregates and greatly extending the volume of the intense decomposition processes. This microheterogeneity has important implications for the spatial and temporal dynamics of the organic-matter field in aquatic ecosystems and for our understanding of how heterotrophic organisms are involved in the decomposition of organic matter. The significance of aggregate-associated microbial processes as key processes and also for the overall decomposition and flux of organic mattervaries greatly among the various systems, and is greatly affected by the total amount of suspended particulate matter. A conclusion from the presented studies and results is that the significance of bacteria for the formation and decomposition of aggregates appears to be much greater than previously estimated. For a better understanding of the functioning of aquatic ecosystems it is of great importance to include aggregate-associated processes in ecosystem modeling approaches.

No abstract

We examined bacterial dynamics in batch cultures of two axenic marine diatoms (Thalassiosira rotula and Skeletonema costatum). The axenic diatoms were inoculated with natural bacterial assemblages and monitored by 4,6-diamidino-2-phenolindole (DAPI) counts, denaturing gradient gel electrophoresis (DGGE) with subsequent analysis of excised, sequenced 16S rRNA gene fragments, and fluorescence in situ hybridization (FISH) with group-specific 16S rRNA oligonucleotide probes. Our results show that algal growth exhibited pronounced differences in axenic treatments and when bacteria were present. Bacterial abundance and community structure greatly depended on species, growth and physiological status of even closely related algae. Free-living and phytoplankton-associated bacteria were very different from each other and were dominated by distinct phylogenetic groups. The diatom-associated bacteria mainly belonged to the Flavobacteria-Sphingobacteria group of the Bacteroidetes phylum whereas free-living bacteria, which were rather similar in both cultures, comprised mainly of members of the Roseobacter group of alpha-Proteobacteria. Presence and disappearance of specific bacteria during algal growth indicated pronounced differences in environmental conditions over time and selection of bacteria highly adapted to the changing conditions. Tight interactions between marine bacteria and diatoms appear to be important for the decomposition of organic matter and nutrient cycling in the sea.

Due to worldwide distribution, high abundance and availability of physiologically diverse isolates the Roseobacter clade is one of the most intensively studied groups of marine bacteria. Organisms of this clade have been detected in a large variety of habitats, from coastal regions to deep-sea sediments and from polar ice to tropical latitudes, and constitute up to 25% of the total bacterial community. Use of a multitude of organic compounds, sulfur oxidation, aerobic anoxygenic photosynthesis, oxidation of carbon monoxide, DMSP demethylation, and production of secondary metabolites are some of the important traits found in this clade. Physiological characteristics and the different isolation sources indicate that organisms of the Roseobacter clade occupy various ecological niches. Since the first description of Roseobacter spp. in 1991, 38 affiliated and validated genera have been described. More than half of these descriptions have been published within the last 3 years. Genome sequencing of currently 40 different strains demonstrates enormous interest in the genetic and metabolic diversity of these bacteria. Plasmids with an enormous size range are also widespread in the Roseobacter clade indicating an adaptive genomic structure. Comparisons with other highly relevant groups, like the SAR11 clade, have shown drastic differences in genome organization.

Dinoroseobacter shibae DFL12T , a member of the globally important marine Roseobacter clade, comprises symbionts of cosmopolitan marine microalgae, including toxic dinoflagellates. Its annotated 4 417 868 bp genome sequence revealed a possible advantage of this symbiosis for the algal host. D. shibae DFL12T is able to synthesize the vitamins B 1 and B 12 for which its host is auxotrophic. Two pathways for the de novo synthesis of vitamin B 12 are present, one requiring oxygen and the other an oxygen-independent pathway. The de novo synthesis of vitamin B 12 was confirmed to be functional, and D. shibae DFL12T was shown to provide the growth-limiting vitamins B 1 and B 12 to its dinoflagellate host. The Roseobacter clade has been considered to comprise obligate aerobic bacteria. However, D. shibae DFL12 T is able to grow anaerobically using the alternative electron acceptors nitrate and dimethylsulfoxide; it has the arginine deiminase survival fermentation pathway and a complex oxygen-dependent Fnr (fumarate and nitrate reduction) regulon. Many of these traits are shared with other members of the Roseobacter clade. D. shibae DFL12 T has five plasmids, showing examples for vertical recruitment of chromosomal genes (thiC) and horizontal gene transfer (cox genes, gene cluster of 47 kb) possibly by conjugation (vir gene cluster). The long-range (80%) synteny between two sister plasmids provides insights into the emergence of novel plasmids. D. shibae DFL12 T shows the most complex viral defense system of all Rhodobacterales sequenced to date.

Bacterioplankton phylotypes of alpha-Proteobacteria have been detected in various marine regions, but systematic biogeographical studies of their global distribution are missing. Alpha-Proteobacteria comprise one of the largest fractions of heterotrophic marine bacteria and include two clades, SAR11 and Roseobacter, which account for 26 and 16% of 16S ribosomal RNA gene clones retrieved from marine bacterioplankton. The SAR11 clade attracted much interest because related 16S rRNA gene clones were among the first groups of marine bacteria to be identified by cultivation-independent approaches and appear to dominate subtropical surface bacterioplankton communities. Here we report on the global distribution of a newly discovered cluster affiliated to the Roseobacter clade, comprising only as-yet-uncultured phylotypes. Bacteria of this cluster occur from temperate to polar regions with highest abundance in the Southern Ocean, but not in tropical and subtropical regions. Between the south Atlantic subtropical front and Antarctica, we detected two distinct phylotypes, one north and one south of the polar front, indicating that two adjacent but different oceanic provinces allow the persistence of distinct but closely related phylotypes. These results suggest that the global distribution of major marine bacterioplankton components is related to oceanic water masses and controlled by their environmental and biogeochemical properties.

Marine Rhodobacteraceae (Alphaproteobacteria) are key players of biogeochemical cycling, comprise up to 30% of bacterial communities in pelagic environments and are often mutualists of eukaryotes. As ‘Roseobacter clade', these ‘roseobacters' are assumed to be monophyletic, but non-marine Rhodobacteraceae have not yet been included in phylogenomic analyses. Therefore, we analysed 106 genome sequences, particularly emphasizing gene sampling and its effect on phylogenetic stability, and investigated relationships between marine versus non-marine habitat, evolutionary origin and genomic adaptations. Our analyses, providing no unequivocal evidence for the monophyly of roseobacters, indicate several shifts between marine and non-marine habitats that occurred independently and were accompanied by characteristic changes in genomic content of orthologs, enzymes and metabolic pathways. Non-marine Rhodobacteraceae gained high-affinity transporters to cope with much lower sulphate concentrations and lost genes related to the reduced sodium chloride and organohalogen concentrations in their habitats. Marine Rhodobacteraceae gained genes required for fucoidan desulphonation and synthesis of the plant hormone indole 3-acetic acid and the compatible solutes ectoin and carnitin. However, neither plasmid composition, even though typical for the family, nor the degree of oligotrophy shows a systematic difference between marine and non-marine Rhodobacteraceae. We suggest the operational term ‘Roseobacter group' for the marine Rhodobacteraceae strains.